REFERENCE: Yunis JJ, Garcia O, Baena A, Arboleda G, Uriarte
I, and Yunis E. Population frequency for the short tandem repeat
loci D18S849, D3S1744, and D12S1090 in Caucasian-Mestizo and
African descent populations of Colombia. J Forensic Sci 2000;45
ABSTRACT: Blood samples from 489 unrelated Caucasian Mes-
tizo and 252 individuals of African descent in Colombia were am-
plified and typed for three short tandem repeat (STR) markers
(D12S1090, D3S1744, and D18S849). All markers conformed to
Hardy-Weinberg equilibrium expectations in both populations stud-
ied. In addition, heterozygosity, mean exclusion chance, polymor-
phism information content, discrimination power, and the assump-
tion of independence within and between loci were determined. The
mean exclusion chance for all three STR markers is 0.9750 in the
Caucasian Mestizo population and 0.9731 in the African Colombian
Population. The discrimination power is 0.999925 and 0.999911 in
the Caucasian Mestizo and African Colombian respectively.
KEYWORDS: forensic science, DNA typing, polymerase chain
reaction, short tandem repeats, population genetics, D12S1090,
D3S1744, D18S849, Colombia
In South America, few STR studies have been done for native,
Mestizo populations (1–3), and South American Black populations
(4), although many studies of STR profiles have been carried out for
the ancestral Spanish and Portuguese populations (5–9). Colombia
is a multi-ethnic and multi-cultural country with near 41 million
people composed of three ethnic groups (10), the Caucasian-Mes-
tizo population representing the largest group followed by the Black
population of African origin and the Amerindian populations (83
ethnic groups). The Caucasian-Mestizo population is composed of
Spanish descent and in a lesser extent of other European, Arabs and
Jewish populations among others and is located in the Andean re-
gion of Colombia and in a lesser extent in the Caribbean plains, Pa-
cific and Amazonian regions. The Black population is located in the
Pacific and Caribbean regions of the country (11,12). The ancestors
of the Black population of Colombia were brought as slaves from
the west coast of Guinea, Ivory Coast, Senegal, and Mali in Africa
to present day Colombia between 1580 and 1650 to work in the
fields and mines (13). By 1800, around 210,000 individuals of
African descent (14) were living in the country, in the Caribbean and
pacific coasts of Colombia. In 1993 a total of 502,343 individuals
(1.5% of the population) were counted (10) as Blacks.
We present the population frequencies of three polymorphic STR
loci analyzed in two major Colombian populations named
D12S1090 (n⫽486 Caucasian-Mestizo; n⫽248 Blacks),
D3S1744 (n⫽484 Caucasian-Mestizo; n⫽252 Blacks) and
D18S849 (n⫽489 Caucasian Mestizo; n⫽250 Blacks). The pop-
ulation frequencies obtained from these markers, not only are im-
portant for forensic science and paternity testing studies, but to char-
acterize genetically the Colombian population and sub-populations.
Materials and Methods
Whole blood was obtained from unrelated Caucasian-Mestizo
individuals from the Andean Region of Colombia requesting pa-
ternity testing studies and from unrelated individuals of African de-
scent collected in five different towns (around 50 individuals from
each town) of the Choco department in the Pacific region of
Colombia. Informed consent was obtained before drawing the
blood samples. The selection of the African descent individuals
was based on the fact that at least two generations did not have ad-
mixture with Caucasian or Amerindians based on interrogation at
the moment of the sample collection. None of these samples are
presumed to be from first-degree relatives.
Genomic DNA was isolated from whole blood by the Quick
Light DNA isolation kit (Lifecodes Corporation, Stamford, CT)
or by the Wizard Genomic DNA isolation kit (Promega Corpora-
tion, Madison, WI) following the manufacturer’s recommenda-
tions. The D12S1090, D3S1744, and D18S849 loci were ampli-
fied by PCR in a multiplex format using the Multiplex I kit
(Lifecodes Corporation, Stamford, CT) in a PTC100VG thermo-
cycler (MJ Research, Watertown, MA) following the manufactur-
ers protocols. The PCR products were resolved in a 4% Acryl-
Juan J. Yunis,
M.D.; Oscar Garcia,
M.Sc.; Andres Baena,
B.S.; Gonzalo Arboleda,
M.D.; and Emilio Yunis,
Population Frequency for the Short Tandem
Repeat Loci D18S849, D3S1744, and D12S1090
in Caucasian-Mestizo and African Descent
Populations of Colombia
Servicios Medicos Yunis Turbay y Cia, Ave 22 #42–24, Santa Fé de Bo-
Instituto de Genética, Universidad Nacional de Colombia, Santa Fé de Bo-
Area de Laboratorio Ertzaintza, C/ Avda. Montevideo 3, E-48002 Bilbao,
Received 31 Dec. 1998; and in revised form 5 May 1999; accepted 25 June
Copyright © 2000 by ASTM International
430 JOURNAL OF FORENSIC SCIENCES
amide-Bis-Acrylamide denaturing gel at 2000 V/1 h and detected
by silver nitrate staining (15) and manually interpreted by two
persons. Allele designations were based on the allelic ladder pro-
vided by the manufacturer.
Statistical evaluations were performed using the HWE-Analysis
software package (HWE-Analysis, Version 3.3. Christoph Puers,
Institute of Legal Medicine, University of Münster). Analyses in-
cluded the possible divergence from Hardy-Weinberg expectations
and other parameters of forensic importance: observed and ex-
pected heterozygosity (16), mean exclusion chance (MEC) (17),
mean paternity exclusion probability (MEP) (18), polymorphic in-
formation content (PIC) (19), and discrimination power (DP) (20).
In addition the GDA computer program (Lewis, P.O., Zaykin,
D. 1999. Genetic Data Analysis. Computer program for the analy-
sis of allelic data. Version 1.0 (d12), free program distributed
by the authors over the internet from the GDA Home Page at
http//chee.unm.edu /gda/), was used to analyze the possible associ-
ations between loci.
Results and Discussion
Table 1 shows the allele frequency distribution for D12S1090,
D3S1744, and D18S849 in the Caucasian-Mestizo and African de-
scent individuals of Colombia. In addition, minimum allele frequen-
cies for PCR based loci based on statistical and populations genetics
theory were determined (21–23) (Table 1). Therefore, a greater con-
fidence with current size databases can be attained for DNA profile
frequency estimates in forensic casework. Also, the results of the dif-
ferent test procedures to determine the correspondence of the geno-
type frequencies with their Hardy-Weinberg equilibrium are shown.
All markers were found to be in HW equilibrium by all three test
-test, the logarithmic likelihood ratio (G test) and exact test)
(24). An interclass correlation test analysis demonstrated that there is
no evidence of associations between any pair of loci in any of these
two populations (data not shown), as should be expected when inde-
pendent loci in different chromosomes are analyzed.
To evaluate the differences between these two populations, a R
⫻C contingency table was used (data not shown). The allele fre-
quency distribution for locus D3S1744 did not show any statistical
significant difference between these two populations (0.1 ⬍p⬍
0.2). Statistical significant differences were detected for locus
D12S1090 and D18S849 (p⬍0.0005). A similar comparison (data
not shown) was carried out between the Colombian Caucasian
Mestizo population and the USA Caucasian population, between
the Colombian Caucasian Mestizo and the USA Hispanics (re-
ported by the manufacturer) and between Black population from
Colombia and Blacks from the USA (17) showing no statistically
significant differences between them.
No statistical significant differences were observed when R ⫻C
tables were used to compare the data obtained from the five differ-
ent towns of the Choco department sampled despite the low num-
ber of individuals analyzed (data not shown). This findings could
TABLE 1—Observed allele frequencies and tests for Hardy-Weinberg equilibrium for D18S849, D3S1744, and D12S1090 loci, in Caucasian-Mestizos
and Black individuals from Colombia.
Caucasian Caucasian Caucasian
Mestizo Mestizo Mestizo Blacks Blacks Blacks
n⫽489 n⫽484 n⫽486 n⫽250 n⫽252 n⫽248
Allele D18S849 D3S1744 D12S1090 D18S849 D3S1744 D12S1090
9 0.001 0.069 0.062 0.022
10 0.017 0.010
11 0.001 0.053 0.004 0.057
12 0.003 0.063 0.016 0.111
13 0.010 0.034 0.006 0.036
14 0.048 0.004 0.045 0.020 0.002 0.042
15 0.212 0.096 0.012 0.218 0.066 0.012
16 0.408 0.084 0.006 0.390 0.089 0.002
17 0.197 0.142 0.004 0.192 0.173 0.012
18 0.095 0.367 0.018 0.086 0.365 0.020
19 0.022 0.173 0.055 0.006 0.175 0.050
20 0.003 0.101 0.083 0.079 0.099
21 0.027 0.076 0.042 0.093
22 0.007 0.108 0.006 0.119
23 0.066 0.004 0.061
24 0.066 0.034
25 0.058 0.057
26 0.077 0.046
27 0.060 0.038
28 0.011 0.008
29 0.012 0.032
30 0.007 0.020
32 0.001 0.002
Frec.min 0.006 0.006 0.007 0.011 0.012 0.014
HET obs. 26 29 141 23 27 116
HET EX. SE. 24.34 ⫾4.31 27.33 ⫾3.46 144.37 ⫾10.91 23.11 ⫾4.41 24.95 ⫾3.84 114.78 ⫾12.72
Homo obs. 5 6 14 5 6 9
Homo EX. SE 4.93 ⫾1.31 6.28 ⫾1.06 12.07 ⫾2.91 4.63 ⫾1.43 5.69 ⫾1.69 8.18 ⫾3.35
test 0.147 0.200 0.463 0.908 0.939 0.377
G test 0.116 0.196 0.412 0.931 0.923 0.148
Exact test 0.055 0.118 0.472 0.952 0.802 0.127
be due in part to a process of genetic “homogenization” carried out
by the slavers in Colombia (13). In that process, individuals speak-
ing the same language were separated in order to avoid emancipa-
tion movements among the slaves. A similar result was obtained
comparing Black populations of Brazil and Venezuela (4). This ad-
mixture process will limit the usefulness of STR markers to trace
back the origin of the Colombian Black population with their spe-
cific African ancestors.
Table 2 shows several parameters of statistical importance for
the loci studied in the Caucasian Mestizo and Black populations of
Colombia such as observed and expected heterozygosity, mean ex-
clusion chance (MEC), mean paternity exclusion (MEP), polymor-
phic information content (PIC) and discrimination power (DP).
Similar results were obtained in both populations for the observed
heterozygosity, MEC, and DP.
In summary, the population frequency of Caucasian-Mestizo
and African Colombians has been established for STR loci
D12S1090, D3S1744, and D18S849. All STR loci were found to be
in HW equilibrium. The combined power of exclusion is estimated
as 0.9750 in the Caucasian Mestizo and 0.9731 in the African
Colombian population. The results obtained in this study can be
used to derive estimates of multiple loci profiles frequencies for
forensic purposes, to calculate paternity indexes and the probabil-
ity of paternity in parentage testing studies and to genetically char-
acterize the Colombian population in population studies.
We would like to thank Sandra P. Moreno, Martha Roa, and
Yolanda Gonzalez for their technical assistance.
1. Jorquera H, Budowle B. Chilean population data on ten PCR-based loci.
J Forensic Sci 1998;43:171–3.
2. Gene M, Fuentes M, Huguet E, Pique E, Bert F, Corella A, et al.
Quechua Amerindian population characterized by HLA-DQ alpha,
YNZ22, 3⬘APO B, HUMTHO1, HUMVWA31A polymorphisms. J
Forensic Sci 1998;43:403–5.
3. Sala A, Penacino G, Corach D. Comparison of allele frequencies of
eighth STR loci from Argentinean Amerindian and European popula-
tions. Human Biology 1998;70(5):937–47.
4. Bortolini MC, Da Silva Junior WA, Weimer TDA, Zago MA, De Guerra
DC, Schneider MP, et al. Protein and hypervariable tandem repeat di-
versity in eight African-derived south American populations: inferred re-
lationships do not coincide. Human Biology 1998;70:443–61.
5. Pestoni C, Lareu MV, Rodrigues MS, Muñoz I, Barros F, Carracedo A.
The use of the STRs HUMTHO1, HUMVWA31/A, HUMF13A1, HUM-
FES/FPS, HUMLPL in forensic application: validation studies and pop-
ulation data for Galicia (NW Spain). Int J Legal Med 1995;107:283–90.
6. Crespillo M, Luque JA, Fernández R, Ramirez E, Garcia P, Valverde JL.
Allele frequency distribution of 13 PCR-based systems in a population
from North-East Spain. Int J Legal Med 1997;110:223–5.
7. Garcia O, Martin P, Budowle B, Uriarte J, Albarrán C, Alonso A. Basque
Country autochthonous population data on 7 short tandem repeat loci. Int
J Legal Med 111. 1998;162–4.
8. Martin P, Alonso A, Budowle B, Albarrán C, Garcia O, Sancho M. Span-
ish population data on 7 tetrameric short tandem repeat loci. Int J Legal
Med 108. 1995;145–9.
9. Gene M, Carracedo A, Huguet E, Perez-Perez A, Moreno P. Population
genetics of the D12S391, CSF1PO and TPOX loci in Catalonia (North-
east Spain). Int J Legal Med 111. 1998;52–4.
10. Departamento Administrativo Nacional de Estadística, DANE (1996).
Censo 1993, Resumen Nacional. Población ajustada y proyecciones.
Santa Fé de Bogotá, República de Colombia.
11. Departamento Administrativo Nacional de Estadística, DANE 1998. Los
grupos étnicos de Colombia en el censo de 1993. Memorias. Santa Fé de
Bogotá, República de Colombia.
12. Sandoval C, De la Hoz A, Yunis E. Estructura genética de la Población
Colombiana. Análisis de Mestizaje. Rev Fac Med UN Col 1993;41:
13. Gutierrez I. Historia del Negro en Colombia. Bogotá. Nueva America,
14. Tannenbaum F. El Negro en las Américas. Esclavo y Ciudadano. Edito-
rial Paidos, Buenos Aires. 1968.
15. Bassam BJ, Caetano-Anolles G, Gresshoff PM. Fast and sensitive silver
staining of DNA in polyacrylamide gels. Anal Biochem 1991;196:80.
16. Nei M. Estimation of average heterozygosity and genetic distance from
a small number of individuals. Genetics 1978;89:583–90.
17. Wiegand P, Budowle B, Rand S, Brinkmann B. Forensic validation of
the STR systems SE33 and TC11. Int J Legal Med 1993;105:315–20.
18. Brenner C, Morris J. Paternity index calculations in single locus hyper-
variable DNA probes: validation and other studies. In: Proceedings of
the international symposium on human identification. Promega Corpo-
ration, Madison WI, 1990;21–53.
19. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic
linkage map in man using restriction fragment length polymorphisms.
Am J Hum Genet 1980;32:314–31.
20. Jones DA. Blood samples: probabilities of discriminations. J Forensic
Sci Soc 1972;12:355–9.
21. Budowle B, Monson KL, Chakraborty R. Estimating minimum allele
frequencies for DNA profile frequency estimates for PCR-based loci. Int
J Legal Med 1996;108:173–6.
22. Chakraborty R. Sample size requirements for addressing the population
genetic issues of forensic use of DNA typing. Hum Biology 1992;64:
23. Weir BS. Independence of VNTR alleles defined by fixed bins. Genetics
24. Guo SW, Thompson EA. Performing the exact test of Hardy-Weinberg
proportion for multiple alleles. Biometrics 1992;48:361–72.
Additional information and reprint requests:
Juan J. Yunis, M.D.
Instituto de Genética
Universidad Nacional de Colombia
Santa Fé de Bogotá, Colombia.
YUNIS ET AL. • POPULATION FREQUENCY 431
TABLE 2—Statistical parameters of forensic importance for D12S1090, D3S1744, and D18S849 loci in Caucasian Mestizo and Blacks from Colombia.
Caucasian Caucasian Caucasian
Mestizo Mestizo Mestizo Blacks Blacks Blacks
Locus D18S849 D3S1744 D12S1090 D18S849 D3S1744 D12S1090
HET obs 0.714 0.775 0.930 0.732 0.774 0.944
MEC 0.519 0.604 0.869 0.539 0.599 0.862
MEP 0.491 0.579 0.870 0.515 0.576 0.865
PIC 0.701 0.763 0.932 0.717 0.760 0.928
DP 0.892 0.929 0.990 0.908 0.927 0.987
Caucasian Mestizo Blacks
MEC Total 0.9750 0.9731
DP total 0.999925 0.999911